Base stacking makes an important contribution to the structure and stability of DNA and RNA.  Previous work has demonstrated the importance of geometry optimization in determining base stacking energies in A-form and B-form DNA.  In this work, we will use symmetry-adapted perturbation theory (SAPT) to analyze the energy contributions to the overall stacking energies for all possible DNA base stack sequences.  The sequence dependence of changes in the energy contributions will be analyzed.

Impact of geometry optimization on base-base stacking interactions:  An energy decomposition analysis

251st National Meeting (2016)

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